German Chancellor Angela Merkel attends news conference after the European Union summit- the first one since Britain voted to quit- in Bratislava, Slovakia, September 16, 2016. REUTERS/Leonhard Foeger

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By Michael Nienaber and Madeline Chambers

BERLIN (Reuters) - German Chancellor Angela Merkel's CDU party suffered its second electoral blow in two weeks on Sunday, slumping to its lowest level since 1990 in a Berlin state vote that rejected her open-door refugee policy.

Voters turned to the anti-immigrant Alternative for Germany (AfD), which with 12.9 percent of the vote will enter its 10th regional assembly among the country's 16 states.

A year before a national election, the result is set to raise pressure on Merkel and deepen rifts in her conservative camp, with more sniping expected from her CSU allies in Bavaria.

The CSU's Bavarian finance minister Markus Soeder was quick to call it the "second massive wake-up call" in two weeks.

"A long-term and massive loss in trust among traditional voters threatens the conservative bloc," he told the Bild daily, adding Merkel's right-left national coalition had to win back support by changing course on its immigration policy.

Merkel's Christian Democrats were routed in the eastern state of Mecklenburg-Vorpommern two weeks ago, triggering calls from the CSU for her to toughen up her migrant policy.

In particular, they want a cap of 200,000 refugees per year, which Merkel rejects.

The secretary general of Merkel's CDU, Peter Tauber, partly blamed the CSU for the losses in Berlin, which only 27 years ago was the front line of the Cold War.

"If there is a dispute within the conservative bloc, it doesn't help us on the ground - especially if this dispute is carried out in the way it is being done from Munich," he said.

A backlash against her migrant policy has raised questions about whether Merkel, Europe's most powerful leader, will stand for a fourth term next year. Given a dearth of options in her party, however, she is still the most likely candidate.

SPD KEEP CONTROL BUT SUPPORT DOWN

Projections from broadcaster ZDF put Merkel's Christian Democrats on 18 percent, down from 23.3 percent in the last election in Berlin in 2011.

The Social Democrats (SPD) also lost support, falling to 22.4 percent from 28.3 percent, but remained the biggest party and are likely to ditch the CDU from their current coalition.

The losses for both the biggest parties point to the further fragmentation of Germany's political landscape, raising the possibility of different coalitions in future.

The SPD, Merkel's junior coalition partner at the national level, wants to form a coalition with the Greens and possibly the radical Left party in the city-state of Berlin.

The Greens won 15.9 percent of the Berlin vote, down 1.7 percentage points from 2011, while the Left party was up 4 points at 15.7 percent, according to ZDF.

The AfD, founded in 2013 as an anti-euro party, was the big winner. It has in the last year played to voters' fears about the integration of the roughly one million migrants who entered Germany last year.

"From zero to double digits, that's unique for Berlin. The grand coalition has been voted out - not yet at the national level, but that will happen next year," said AfD candidate Georg Pazderski to cheering supporters after the results.

Commentators said the result indicated that the party looked poised to enter the lower house of parliament in 2017.

"With the Berlin result, the AfD has consolidated its position and shown it can appeal to voters across the board - it is now represented in a big city, eastern German states and in more affluent western states like Baden-Wuerttemberg," said Thomas Jaeger, political scientist at Cologne University.